nwfscDiscard.RmdThe nwfscDiscard package was written by scientists at the Northwest Fisheries Science Center (NWFSC) to explore and process West Coast Groundfish Observer Program (WCGOP) data. This package can be used to process WCGOP data for West Coast groundfish assessments.
nwfscDiscard can be used to:
Ensure confidentiality is met based on the requested stratification of data by gear and area.
Summarize observed discard rates by gear and area for catch share and non- catch share vessels.
Summarize biological data from observed discards for use in groundfish stock assessments.
Visualize data.
The code combines the data into fleet structures requested by users based on gear and areas. The gear and area grouping are passed to all of the processing functions:
# Gears to keep and how they should be grouped within a list:
gear_groups <- list(c("Bottom Trawl", "Midwater Trawl", "Shrimp Trawl"), c("Hook & Line", "Pot"))
gear_names <- c("trawl", "fixed gear")
# Fleet areas:
fleet_groups <- list(c("WA", "OR", "CA"))
fleet_names <- c("coastwide")where the above code groups the data into two coastwide fleets based upon gear types. The data can be grouped by state or by latitude. The WCGOP data contains both a departure and return states. Generally, the return state is used to group data based on state areas. If the data area being grouped by latitude this can be done by using the latitude of the set (SET_LAT), the average latitude across a set (AVG_LAT), or by the latitude that the gear was retreived (UP_LAT). If the data needs to be split north and south of 40 10 N. latitude, the WCGOP data contains a field that specifies north or south based on the average latitude (AREA). Since the data can be split across various fields (state or latitude) the column name to specify the grouping needs to be specified:
fleet_colname = "r_state"where the above example groups the data based on the return state. The fleet column name should be a column in the data.
Currently, there are a couple of functions that provide summaries and plots of the data to help users. The first is a function that pull data from the GEMM which has expanded catches based on the retained and discard observations by WCGOP. The catch by sector is then summarized by sectors that are catch shares or non-catch shares. This information could be used to better inform how the rates between the groups could be combined for use in an assessment (e.g., are the majority of catches occurring by catch share vessels?).
gemm <- nwfscSurvey(common_name = "Sablefish")
gemm_check <- calc_prop_gemm_catch(
data = gemm,
species_name = "Sablefish"
)Visualize the discard length or ages by gear type or catch share vs. non-catch shares:
wcgop_bio <- plot_wcgop_bio(
data = biological_data,
species_name = "Sablefish",
plot = 1:2,
comp_column = "length"
)Once the grouping has been specified, the data are checked to ensure the grouping can meet confidentiality rules. This check based on all the data within the specified grouping, not just the observations of a particular species.
ci <- check_confidential(
data = catch_data,
gear_groups = gear_groups,
gear_names = gear_names,
fleet_colname = fleet_colname,
fleet_groups = fleet_groups,
fleet_names = fleet_names
)The length and or age compositions of discarded fish can be the processed for use in assessment.
bio_data <- get_biological_data(
data = biological_data,
catch_data = catch_data,
species_name = "Sablefish",
len_bins = seq(20, 90, 2),
age_bins = 1:50,
gear_groups = gear_groups,
gear_names = gear_names,
fleet_colname = fleet_colname,
fleet_groups = fleet_groups,
fleet_names = fleet_names
)where the species name, length, and age bins need to be provided.
The mean weight of the discarded fish can also be calculated for using in an assessment:
mean_weight <- get_mean_weights(
data = catch_data,
species_name = "Sablefish",
gear_groups = gear_groups,
gear_names = gear_names,
fleet_colname = fleet_colname,
fleet_groups = fleet_groups,
fleet_names = fleet_names
)The observed catch are then processed for discard rates or totals.
Data from catch share and non-catch share vessels are processed
separately based on attributes of the data. Catch share vessels have 100
percent observer coverage starting in 2011 and are treated as a census
of discarding in the IFQ fishery.
Non-catch share vessels have variable rates of observer coverage and the
discard rates are based on the observed trips. These trips are then
bootstrap to estimate uncertainty around the discard rates.
ob_out <- do_discard_bootstrap(
data = catch_data,
species_name = "Sablefish",
boot_number = 10000,
gear_groups = gear_groups,
gear_names = gear_names,
fleet_colname = fleet_colname,
fleet_groups = fleet_groups,
fleet_names = fleet_names,
seed_number = 1,
rm_em_data = TRUE
)Additionally, a subset of catch share vessels use electronic monitoring (EM) rather that have a physical observer onboard for all trips. These vessels have specific rules about what they can and cannot be discarded at-sea and which species need to be recorded in the logbook and/or monitored by video. The EM program manual can be found online and includes a list of IFQ species. All IFQ species can be discarded at sea within view of cameras. If appropriate, the discard from EM vessels can be processed and are treated as a census of discarding. A subset of trips for vessels that use EM will have a physical onboard observer and be included in the catch records. If EM discards are processed and added to the observed non-EM catch share discards, one must exclude the physical onobard observer data from EM vessels since this would duplicate records.
em_out <- do_discard_bootstrap(
dir = here::here(),
data = em_catch_data,
species_name = "Sablefish",
gear_groups = gear_groups,
gear_names = gear_names,
fleet_colname = fleet_colname,
fleet_groups = fleet_groups,
fleet_names = fleet_names
)The discard rates from the catch share vessels with onboard observers and EM observation can be then combined:
combine_cs_discards(
cs_data = ob_out$cs,
em_data = em_out$em
)Description of data products:
Confidentiality Checks:
confidentiality_catch_share.csv: The number of observed vessels, trips, hauls, and observations on non-catch and catch-share vessels of selected species given the request data stratification by area and gear type. To meet confidentiality a total of three or more vessels must be observed by stratification and year.
confidentiality_em_catch_share.csv: The number of observed vessels, trips, hauls, and observations on vessels using electronic monitoring (EM) of selected species given the request data stratification by area and gear type. To meet confidentiality a total of three or more vessels must be observed by stratification and year. The confidentiality check for EM vessels is separate from the previous confidentiality check since the EM data are in a separate data file given the unique nature of the data. The EM program began in 2015 and is limited to catch-share vessels with participation increasing in recent years.
Biological Data:
biological_discard_lengths.csv and biological_discard_ages.csv: The length/age observations of discarded fish formatted based on requested stratification, data bin structure, and sex. Only select species include sex-specific data within WCGOP. Data are formatted for SS3.
discard_mean_body_weights.csv: The mean body weight in kg of discarded fish. Only years with 30 or more observations by stratification are provided. Data are formatted for SS3.
Discard Rates:
discard_rates_catch_share.csv: The observed discard totals and rates for catch-share vessels. The catch-share fishery has full observer coverage, hence data are considered a census and no measure of uncertainty are provided.
discard_rates_em_catch_share.csv: The observed discard totals and rates for catch-share vessels using EM. These data are considered a census and no measure of uncertainty are provided.
discard_rates_combined_catch_share.csv: The combined discard totals between the catch-share vessels with onboard observers and those using EM. Analysts should use this file when determining how to combine discard rates between catch-share and non-catch share vessels for use in stock assessment.
discard_rates_noncatch_share.csv: The observed discard totals and rates for non-catch share vessels. These data are bootstrapped to estimate median discard rates and standard deviation for use in assessment.